Posted
by
Soulskillon Friday July 13, 2012 @10:14AM
from the you-bred-velocibacteria? dept.

An anonymous reader writes with news that researchers at the Georgia Institute of Technology have taken a gene from 500-million-year-old bacteria and inserted it into modern E. coli bacteria. They then allowed the bacteria to evolve over the course of a thousand generations to see whether it would resemble its original 'evolutionary trajectory.' From the article:
"After achieving the difficult task of placing the ancient gene in the correct chromosomal order and position in place of the modern gene within E. coli, Kaçar produced eight identical bacterial strains and allowed 'ancient life' to re-evolve. This chimeric bacteria composed of both modern and ancient genes survived, but grew about two times slower than its counterpart composed of only modern genes. 'The altered organism wasn’t as healthy or fit as its modern-day version, at least initially,' said Gaucher, 'and this created a perfect scenario that would allow the altered organism to adapt and become more fit as it accumulated mutations with each passing day.' The growth rate eventually increased and, after the first 500 generations, the scientists sequenced the genomes of all eight lineages to determine how the bacteria adapted. Not only did the fitness levels increase to nearly modern-day levels, but also some of the altered lineages actually became healthier than their modern counterpart."

Not only did the fitness levels increase to nearly modern-day levels, but also some of the altered lineages actually became healthier than their modern counterpart.

So yes, one hopes this doesn't get out of the Level 4 Bio Lab.

500 million years ago there were no warm blooded animals, and most life was aquatic [wikipedia.org]. Whereas today, its rare (but not un-heard of) [jst.go.jp] to find an e.coli strain that can live for long outside the gut of a warm blooded animal, clearly this was not the case in the Cambrian.

Chances are this gene is from a time when water born e.coli were the norm.

Oh, I'm sure that in a year or two they'll have ancient gene splicing simple enough that Jeremy Clarkson can do it.I mean, it's just a itsy bitsy teeny weeny bacterium, right? It's not like one of those tiiiny things could do a lot of damage anyhow!

What scares me are the scientists that want to make gemo bugs to fight other harmful bugs. We know what goes wrong every time we try something like that. But this time it's all going to be different. Yeah, rite.

Every time I hear of stuff like this i always think of the same thing...Kudzu [wikipedia.org]. Before my grandmothers passed on we used to talk about what life was like during the depression and both told me how the scientists were just completely sure that kudzu was the answer, why it'd fix the dust bowls and save the farms! Oh it fixed it alright, if you call spreading like a cancer [wordpress.com] a 'fix'.

Let us just hope they are smart enough to keep this shit under lock and key and never ever let it out, because i seriously doubt t

If we are referring to popular culture for ideas about what could go wrong, there is a Canadian show called 'Regenesis' which I highly recommend. It is just sciency enough to make it uninteresting to the general public (Canadian accents and US government policy bashing may also play a role). Quote: "There are people working on things in labs right now that make the manhattan project look like kids playing with lego".

It's got a bad case of CSI syndrome, though.How do they do 5 man-years worth of science with four people every two weeks? Oh, right, they're BRILLIANT.

So brilliant that one of them dies in a "freak vortex accident". Because the vortex wasn't 'properly maintained'. Never mind that I've had vortexes that were built in the '80s, never been serviced in any way whatsoever (probably not even cleaned...) and will continue working for 30 more years. Never mind that th

So you are saying the only way to make humans to involve is to create a super bacteria, that will wipe out 75% of the population, because the genes have been dormant for so long that we have no resistance to the new mutations.

Or perhaps you work for Gorilla Grog and you just want to devolve the human race to Gorilla's.

When the researchers looked closer, they noticed that every EF-Tu gene did not accumulate mutations. Instead, the modern proteins that interact with the ancient EF-Tu inside of the bacteria had mutated and these mutations were responsible for the rapid adaptation that increased the bacteria’s fitness. In short, the ancient gene has not yet mutated to become more similar to its modern form, but rather, the bacteria found a new evolutionary trajectory to adapt.

“we want to know if an organism’s history limits its future and if evolution always leads to a single, defined point or whether evolution has multiple solutions to a given problem.”

I would wager it would almost have to be the latter. For example, I found it odd that the article made no mention of horizontal gene transfer [wikipedia.org] and how, over 500 million years, the chance of that bacteria participating in HGT with a distantly related bacteria could have given it, say, a faster growth mechanism -- just like bacterial resistance to drugs is theorized to be a result of HGT. This is probably a useful experiment to look at one of the many mechanisms of evolution but not the entire picture of evolution nor could it effectively draw a final conclusion that "evolution always leads to a single, defined point."

It appears the experiment already has proven that evolution can take many tracks, as the bacteria adapted to the ancient gene, and did not mutate the ancient gene at all as of yet. Sounds to me like the evolutionary track has already altered, and if the bacteria is as healthy or more so than its unaltered cousins, then this bacteria would already be in better shape on the evolutionary ladder and would push evolution in a different direction.

why take chances with ancient specimens? Couldn't they have learned the exact same things using more modern and better understood strains? Don't get me wrong. I love science and discovery and all that jazz. I just wonder about the playing with fire mentality of some researchers sometimes. "Hey we're gonna do this cool experiment, let's do it with something really COOL!"

Couldn't they have learned the exact same things using more modern and better understood strains?

As I read the article, that's what they did. The 500 million year old part appears to be hype; apparently they calculated what the genes would've looked like early in the evolution of the species and recreated part of it to watch it evolve again. But I might be wrong there, but I don't think they did it just because it seemed COOL to grow E. coli bacteria (we all do that already).

My wife had a terrible MRSA infection a few years ago that got so severe she had to be put on intravenous antibiotics twice a day for nearly two weeks. She had to take some supplements that aided in keeping the proper flora counts in her intestine because the strong antibiotic was wiping them out. My cousin had to go through the same thing after he suffered a burst appendix, and they pumped his system full of antibiotics to stave off sepsis. The hospital fed him a lot o

Not only in the summary here on/. horrible, but the PR... is even worse.
Where's the link to the peer-reviewed work? Neither in the "summary", nor in the PR.
FWIW, I don't find the purported results interesting in the slightest in their current form.
For example, how were the cells grown? (please don't say in LB in a chemostat.)

Arslan BK and Gaucher EA Replaying the Tape of Life Through Experimental Evolution of Ancient EF-Tu proteins Astrobiology Science Conference 2010: Evolution and Life: Surviving Catastrophes and Extremes on Earth and Beyond, held April 26-20, 2010 in League City, Texas. LPI Contribution No. 1538

Which I think was just a presentation that provides very little information given all I can find is this PDF [usra.edu]:

Whether evolution would ‘replay the
tape of life’ if given the opportunity has long fascinated
biologists. Paleogenetics via laboratory resurrected
ancient genes not only reveals information regarding
ancestral phenotypes and environments but
also provides an opportunity to ‘replay’ the molecular
tape of life. Recent work has demonstrated that ancestral
sequences can be computationally determined and
experimentally resurrected. The ideal paleoexperimental
evolution system requires an organism
with a short generation time and a protein whose ancestral
genotype and phenotype used to replace the
modern gene and causes the modern host to be less fit.
The research described here focuses on Elongation
Factor Tu (EF-Tu) involved in the protein synthesis
machinery of both eukaryotic and prokaryotic organisms.
The optimal thermostability of EF-Tus correlates
with the optimal thermostability of their host organisms
and are ideal for these types of experiments. Previously
we have resurrected ancient EF-Tus and
showed that these ancient proteins display a range of
thermostability profiles. We will replace the modern
EF-Tu sequences with ancient EF-Tus and observe
their adaptation through experimental evolution. Results
from this work will help us identify whether evolution
is repetitive for this experimental system.

I don't think that really answers your question and I think this research has only been presented at conferences, published in conference proceedings and not yet peer reviewed in a journal (if it has there is no mention of it on Kacar's CV). I also find it odd that on her site she's using the phrase "tree of life" and not "web of life" which I thought was a more modern way of looking at evolution -- especially in prokaryotes.

I will say that it is probably within line to chide the researcher for putting this little blurb on her research page [gatech.edu]:

Experimental Evolution of Ancient Proteins

To assess the role of contingency in evolution, I construct an experimental time machine in the lab by inserting previously resurrected genes into a modern bacterial genomes, then subjecting them to experimental evolution. Observing the real-time evolution of ancient genes as they adapt to the conditions of modern bacteria allows us to analyze evolution in action.

"Experimental time machine?" Please, leave the hype and sensationalism to the "science" reporters.

Whether evolution would ‘replay the tape of life’ if given the opportunity has long fascinated biologists. Paleogenetics via laboratory resurrected ancient genes not only reveals information regarding ancestral phenotypes and environments but also provides an opportunity to ‘replay’ the molecular tape of life.

IANAB, but it doesn't make sense to me that this experiment does what she is claiming. I can understand learning about "ancestral phenotypes", but "replay the molecular tape of life"? That would only be possible if the cells were exposed to the same conditions they would have 500 million years ago, correct? With environmental conditions being a chaotic system, you'd have to get it exactly right-- impossible given we don't have an exact knowledge of those conditions. At best you might argue that you can show

"Experimental time machine?" Please, leave the hype and sensationalism to the "science" reporters.

Have pity on the poor girl. Science and Nature (and the university PR department) keeps telling you how important the public understanding of science is, and how important it is for scientists to explain their work in language the general public can understand. Otherwise you'll lose your grants, the Republicans will teach creationism in school, and your freshman biology students will go blank, fall asleep in class and major in business administration.

I find your claim to be a microbiologist to be questionable. It's a well known fact that women are drawn to the biological sciences, and that no woman reads Slashdot. Therefore your are not a microbiologist.

I was expecting a huge explosion of growth that chases the scientist out of the lab, grabs his ankle with a tentacle, drags him back into the lab to infect him and give him Akira-like telekinetic power and a thirst for world rule

What's amazing in modern society is how so many non-scientists (mainly religious fundamentalists of different sects) think evolution is very much up for debate while problems in physics are totally solved when it's the other way around. I was confronted once by an anti-evolution person who thought exactly how gravity works was a long ago solved case but evolution was some new wacky baseless idea being forced on gullible unbelievers.

The Conservative Judeo-Christian "about 5000-10000 year old universe" crowd doen't all say evolution CAN'T happen, but they all do say that within 6x24 hours of the creation of the Universe, the world looked like that described in Genesis. They don't say that if Rapture doesn't come for another 100,000 years we won't have new species, nor do most say that we don't have species now that didn't exist at the time of Adam and Eve. But for the fact that the sun may expand sooner, I would've used a billion year

In a sense, you're both right. We do have a deep understanding of gravity with very few situations that we cannot calculate, and therefore we now turn to a deeper and more complete understanding. An equivalent problem in biology might be the origin of life in terms of specific chemical reactions. It would be reasonable to say that physics has 'solved' gravity and biology and not 'solved' origin of life, although in both cases scientists don't stop but simply turn to the next level of understanding, with

I think that you'll find the more intelligent ones make a distinction between micro-evolution and macro-evolution.

If they were really intelligent, they would realize that there is no fundamental difference between "micro-evolution" and "macro-evolution". Over a few billion years, "micro-evolution" tends to add up. Eventually you get a population which can no longer interbreed with the original to produce fertile offspring, and a brand new species is born.

The fundamental difference is, to use your words, things need to "add up", and by definition has to remain continually viable with each "addition".

We can argue about the degree of difference, but the standard response there is "no difference" here is essentially the same as saying "There's no difference between winning a coin flip and winning the lottery, they're both just randomness".

Bonus points: Enumerate the set of predictable scientific causal factors that produce the specific values of random in "ra

The fundamental difference is, to use your words, things need to "add up", and by definition has to remain continually viable with each "addition".

I don't know where you got that idea. Many "additions" are fatal during early development; of the rest, they are just as likely, or perhaps more likely, to be harmful or neutral rather than beneficial. If there is a benefit, it may not show up for generations, masquerading as a neutral or even slightly harmful change until the population's environment changes enough to put the mutation in a more positive light.

Of course, the "neutral" mutation could just as easily make it harder to adapt. The thing is, the

Then this cannot be an "addition" in a sequence by which you explain the end result. You either mean a series of sequential changes by "addition", or you don't. If you mean a series of changes, each one must be survivable in itself to the point of reproduction.

The causes of "random mutation" are well-known...

Consider carefully what you are saying here. If you know the exhaustive set of causal factors, and their relative influence, the event is not r

We're really coming to the point in history where the thought of controlling genetic research is not possible. The tools and knowledge on how to do it are widely available. It would be tantamount to controlling computer programers.

Why are we making E. coli bacteria better faster and stronger? I suppose it could lead to implementing the same method in other species, mammals maybe even (which would have some pros and cons about them too). But is that leap in science something we want to make at the cost of making something stronger that could possibly damage humanity? It seems like the risks far out weigh what we would have to gain.

This sounds like an interesting opportunity to study convergent evolution [wikipedia.org]:
1. Put ancient bacteria in different environments, and let their lineages diverge;
2. Move the evolved bacteria to similar environments, and check if they converge;
3. Repeat the experiment with differing numbers of generations spent in different environments. How does the convergence depend on the time spent diverging beforehand?

Well, a defining characteristic of the e. coli species is the lack of an ability to transport citrate across the cell membrane. Enough so that this is often used to differentiate e. coli from salmonella in cultures. So, evolving the ability to transport (and therefore metabolize) citrate in the lab [wikipedia.org] would seem to be a pretty good example of e. coli becoming something other than e. coli (lacking one of the defining characteristics of the species).

It's time to realize that a "defining characteristic" assigned my man is subject to revision.

There was a time that, for a person, having a heartbeat was a defining characteristic of being alive.

We now know no longer consider you dead just because your heart stopped.

Not to mention that some models of artificial hearts or heart-assist devices result in a person who is alive, awake, and functional without a pulse, or at least not one that you would recognize if you put your fingers on the person's wrist.

It's time to realize that a "defining characteristic" assigned by man is subject to revision.

There was a time that, for a person, having a heartbeat was a defining characteristic of being alive.

We now know no longer consider you dead just because your heart stopped.

Not to mention that some models of artificial hearts or heart-assist devices result in a person who is alive, awake, and functional without a pulse, or at least not one that you would recognize if you p

Yes, that's a point that my argument makes by coincidence. All this micro- vs macro- evolution is worthless speculation anyway because nature doesn't work that way. Nature isn't divided neatly from one species to another and none of our working definitions of a species work in every situation. The very idea of a 'species' goes against observational and theoretical reasoning when it comes to evolution because it implies that there's a cutoff point where one generation is species A and the next is species

What more is there to say? I don't understand why people are so vehemently opposed to this simple and readily verifiable explanation for the way that complex systems (like biological life, social structures, economic systems, galaxies, indeed the whole Universe or Universes, etc.) behave.

These are generally people who can't conceive of really big things, really small things and really long times. They think that light speed means "instantaneous". They think the WTC towers should have fallen over on their sides. They can't understand that lighter than air isn't necessarily weightless. They simply cannot imagine the timespans necessary to understand evolution. In their minds, it's an ape giving birth to George Washington.

How about... because it can't possibly evolve higher organisms ? This is a question more and more often posed in biological papers (and I don't mean by creationists, loony or otherwise).

How the hell do organisms that have a generation switch of more than 100.000 times longer than simple lifeforms retain fitness ? A generation length is what determines the "learning rate" of an organism. The human "species" leans once every 20 years, with ~2 billion individuals alive. Most bacteria once every 2 minutes, for

Firstly, I don't see how what you say in any way precludes the evolution of "higher" organisms.

Secondly, I think [random] mutation occurs much more frequently than you'd like to think, especially given that mutation—or, more generally, variation—is more complex than just the changing of gene sequences due to random bursts of radiation from far off supernovae. There are numerous viruses that insert their DNA sequences into infected hosts' DNA sequences, chemicals in the environment and produced b

You never, ever let evolution experiments get to 1001 generations. It ALWAYS turns into Hitler brain in a great white shark. Creationists are so adamantly against evolution because they're trying to protect you.

So if we can trick shark-Hitler into living about 50 generations all in the course of two years, he would think his Thousand Year Reich had actually come and gone, and he would happily go back to being a painter-shark.

Good grief. Where did you learn about science. "Experimentation" doesn't mean just a test tube. You can't, for instance, bottle up a mini galactic supercluster. What you do is you formulate a theory, some of it based on experimentation, a lot of it mathematical models, you make predictions and then you go to your telescopes and attempt to assess whether the predictions are correct or not. You're understanding of science is about that of a five year old.